drug-complex-system-builder
bylearningmatter-mit· 60 skills
Build a solvated, charge-neutralized protein-ligand complex for OpenMM molecular dynamics simulation. Combines a prepared receptor PDB and ligand SDF, parameterizes the ligand with OpenFF Sage or GAFF (AM1-BCC charges), applies Amber ff14SB to the protein, solvates with explicit water, and adds counterions. Use this skill when the user wants to solvate a complex, set up a system for MD, prepare for simulation, add water and ions, or build a simulation box from a protein-ligand structure.
How to install drug-complex-system-builder?
learningmatter-mit/atomisticskills/drug-complex-system-builder
$npx -y skills add learningmatter-mit/atomisticskills --skill drug-complex-system-builderInstalls into the current project.
›Prefer a prompt? Paste this to your agent
Run `npx skills use "https://github.com/learningmatter-mit/atomisticskills" --skill "learningmatter-mit/atomisticskills/drug-complex-system-builder"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/learningmatter-mit/atomisticskills" that are relevant to the current task. Run `npx skills add "https://github.com/learningmatter-mit/atomisticskills"` and select the relevant skills, then follow their instructions.
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